7NE4

E125A mutant of oligopeptidase B from S. proteomaculans with modified hinge region

Summary for 7NE4

• Entry DOI: 10.2210/pdb7ne4/pdb
• Descriptor: Oligopeptidase B, SPERMINE (3 entities in total)
• Functional Keywords: hydrolase
• Biological source: Serratia proteamaculans
• Total number of polymer chains: 1
• Total formula weight: 78870.68

Authors

Petrenko, D.E.,Nikolaeva, A.Y.,Lazarenko, V.A.,Dorovatovskiy, P.V.,Vlaskina, A.V.,Mikhailova, A.G.,Rakitina, T.V.,Timofeev, V.I. (deposition date: 2021-02-03, release date: 2021-03-03, Last modification date: 2024-01-31)

Primary citation

Petrenko, D.E.,Timofeev, V.I.,Britikov, V.V.,Britikova, E.V.,Kleymenov, S.Y.,Vlaskina, A.V.,Kuranova, I.P.,Mikhailova, A.G.,Rakitina, T.V.
First Crystal Structure of Bacterial Oligopeptidase B in an Intermediate State: The Roles of the Hinge Region Modification and Spermine.
Biology (Basel), 10:-, 2021

PubMed Abstract: Oligopeptidase B (OpB) is a two-domain, trypsin-like serine peptidase belonging to the S9 prolyloligopeptidase (POP) family. Two domains are linked by a hinge region that participates in the transition of the enzyme between two major states-closed and open-in which domains and residues of the catalytic triad are located close to each other and separated, respectively. In this study, we described, for the first time, a structure of OpB from bacteria obtained for an enzyme from with a modified hinge region (PSPmod). PSPmod was crystallized in a conformation characterized by a disruption of the catalytic triad together with a domain arrangement intermediate between open and closed states found in crystals of ligand-free and inhibitor-bound POP, respectively. Two additional derivatives of PSPmod were crystallized in the same conformation. Neither wild-type PSP nor its corresponding mutated variants were susceptible to crystallization, indicating that the hinge region modification was key in the crystallization process. The second key factor was suggested to be polyamine spermine since all crystals were grown in its presence. The influences of the hinge region modification and spermine on the conformational state of PSP in solution were evaluated by small-angle X-ray scattering. SAXS showed that, in solution, wild-type PSP adopted the open state, spermine caused the conformational transition to the intermediate state, and spermine-free PSPmod contained molecules in the open and intermediate conformations in dynamic equilibrium.

PubMed: 34681120
DOI: 10.3390/biology10101021

Experimental method

X-RAY DIFFRACTION (2.717 Å)